Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Surface-based registration
by Razlighi, Qolamreza R. 06 Nov '15

06 Nov '15

Hi Guys, I read in the sidenote here (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) that inter-subject surface base registration using mris_register and -1 flag performs a sort of rigid registration. So I tried it between two of my subjects with the command below mris_register -1 -curv P00001639/FreeSurferClean/surf/lh.sphere P00001639/FreeSurferClean/surf/lh.sphere lh.sphere3.reg and got the results (see the attachment). It is clear that the registration output is just a shifted version of the source. Having this confirmed I want to know if there is any way to force the mris_register to perform a complete non-linear surface based registration for inter-subjects registration the same way it does for template. I have to mention that I visualize the lh.sphere3.reg using freeview and loaded the sane lh.curv on that surface. I hope I’m not doing anything stupid. [cid:AEB13CCB-455D-4591-B278-FEF31F6C0B4B@cpmc.columbia.edu] Best -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razlighi(a)gmail.com<mailto:razlighi@gmail.com> Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/

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R: Re: R: Re: average z-score of each subject from a common cluster
by stdp82＠virgilio.it 06 Nov '15

06 Nov '15

I have run mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig.masked. nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum summaryfile and I have obtained 9 columns and 5 rows. I'm confused on results. Where is the mean z-score for cache.th13.neg. sig.masked.nii.gz? # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 -4 7 7.0 Seg-004 -2.4544 0.5023 -3.2164 -1.7619 1.4545 2 -3 153 153.0 Seg-003 -2.6662 1.4724 -6.2120 1.7587 7.9707 3 -2 848 848.0 Seg-002 -2.4930 2.0088 -6.4504 2.3528 8.8032 4 -1 1518 1518.0 Seg-001 -2.1416 1.6727 -6.4227 2.5420 8.9648 5 0 161316 161316.0 Seg0000 1.4152 1.6218 -7.0471 14.1452 21.1923 Because my data are on surface mri_surfcluster should be helpful? Thanks. Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 3-nov-2015 19.55 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: average z-score of each subject from a common cluster > >look in the summaryfile. Also, don't use --seg z.nii.gz. In the command >below, it works because you have --annot afterwards, but in general it >is not correct > >On 10/30/2015 04:22 PM, stdp82(a)virgilio.it wrote: >> Thanks. >> I have obtained: >> >> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >> >> cwd >> >> cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc -- i >> z.nii.gz --sum summaryfile >> >> sysname Darwin >> >> hostname iMac-di-Stefano.local >> >> machine x86_64 >> >> user Stefano >> >> UseRobust 0 >> >> Loading z.nii.gz >> >> Loading z.nii.gz >> >> Voxel Volume is 1 mm^3 >> >> Generating list of segmentation ids >> >> Found 22 segmentations >> >> Computing statistics for each segmentation >> >> 0 -7 2 2.000 >> >> 1 -6 110 110.000 >> >> 2 -5 255 255.000 >> >> 3 -4 518 518.000 >> >> 4 -3 1190 1190.000 >> >> 5 -2 1692 1692.000 >> >> 6 -1 4104 4104.000 >> >> 7 0 61577 61577.000 >> >> 8 1 42598 42598.000 >> >> 9 2 28146 28146.000 >> >> 10 3 14859 14859.000 >> >> 11 4 5845 5845.000 >> >> 12 5 1899 1899.000 >> >> 13 6 485 485.000 >> >> 14 7 116 116.000 >> >> 15 8 75 75.000 >> >> 16 9 74 74.000 >> >> 17 10 78 78.000 >> >> 18 11 65 65.000 >> >> 19 12 104 104.000 >> >> 20 13 45 45.000 >> >> 21 14 5 5.000 >> >> >> How I can know the meaning of this number? Where is z? >> >> I have tried also with: >> >> mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z.nii. gz >> --sum summaryfile --mask >> .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache.th13. neg.sig.masked.nii.gz >> --avgwfvol mrivol >> >> >> but I have problem with interpretation. >> >> >> >> Stefano >> >> >> ----Messaggio originale---- >> Da: greve(a)nmr.mgh.harvard.edu >> Data: 30-ott-2015 16.17 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] average z-score of each subject from a >> common cluster >> >> >> >> On 10/30/15 7:16 AM, stdp82(a)virgilio.it wrote: >>> Hi list, >>> I have two queries, please. >>> >>> I'd like to have the z-score from my rsfMRI data (seed- analyis). >>> >>> 1) I have extract the z-score from the Vtx Max >>> >>> In details, after groups comparison analysis, I have opened >>> the cache.th13.pos.sig.cluster.summary contained in group.diff >>> folder and I have read the Vtx Max coordinates. >>> Next, I have open the z.nii.gz of each subject and I have >>> expected the z-score from the vertex which have the Vtx Max >>> coordinates. >>> >>> Is this procedure corrected? >> Yes >>> >>> 2) z-score of each subject from a common cluster >>> >>> I would like to use the cluster which shows the group difference >>> (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would >>> extract from it the average of the z-score which is contained in >>> each subject. >>> How should I do? >> Use mri_segstats passing the z map as the input (--i) and the >> cluster map as the seg. The output will be --sum. Run with -- help >> for more info >>> >>> Thanks. >>> >>> >>> Stefano >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > >

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mri_convert and large values
by McMains, Stephanie 06 Nov '15

06 Nov '15

We are finding a conversion problem with our latest multiband/SMS data (Using a sequence from Minnesota). The values can be very large, greater than 53,000. These large voxels get turned into very large negative numbers when converting to nii. This happens even if we use the flag –odt float and/or –ns 1. When we use the –odt flag, it does set the output data type to float32, but the values are still wrong. We're using FreeSurfrer 5.3.0 on CentOS 6.5 x86_64. Thanks, Stephanie +++++++++++++++++++++++++ Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138 +++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information…

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Re: [Freesurfer] Recon-all with lower resolution T2 / Proton Density reconstructions and higher res T1
by Ajay Kurani 06 Nov '15

06 Nov '15

Hi Bruce, 1) I was also concerned 3mm may be too thick but I will try a few subjects to see how it goes. 2) Hi Eugenio I wanted to see if you can give a bit of insight into the hippocampal issue. 3) Bruce, sorry for the confusion. I was referring to sqrt(T1w*B1 x T2w*B1) ~ B1 bias field estimate not the T1/T2 myelin mapping. Do you see any forseeable issues of correcting the T1w and T2w image with the B1 estimate prior to running myelin mapping (T1/T2)? Essentially if we remove B1 already then there should not be any additional B1 cancellation when dividing the images. Do you see any issue with using the same B1 bias field to correct resting state data after motion correction is performed? Thanks, Ajay

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Problems with mri_nu_correct.mni
by Emmanuelle Renauld 06 Nov '15

06 Nov '15

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stat/math tools for MGH file
by Yang, Daniel 06 Nov '15

06 Nov '15

Dear FreeSurfer experts, I have a number of *.cluster.mgh files and I would like to calculate their difference and peak coordinate etc like in fslmaths or fslstats in FSL. For example, given two images, I want to know the brain regions in image1 but not in image2. Could you please recommend the general command line tools I can use for these purposes? Many thanks, Daniel

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Cortical thickness in the depth of a sulcus vs on top of a gyrus: Comparison
by Wrobel, Pawel 06 Nov '15

06 Nov '15

Dear FreeSurfer Developers, I have been wondering, if it is possible to compare cortical thickness in the depth of a sulcus with the the cortical thickness on top of the gyrus? I found the curvature maps in subjects' folders but I don't know how to proceed. I would be very thankful for every hint that You could give me. Thank You for Your assistance! Kind regards, Pawel

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Re: [Freesurfer] the matrix
by Douglas Greve 05 Nov '15

05 Nov '15

make sure there are no blank lines On 11/5/15 6:29 PM, Erik Lindberg wrote: > OK, however I tried several options. With the matrix 1 1 1 1 -1 -1 -1 > -1 0 (using the doss option for age) I basically get the same results > > > Reshaping mriglm->mask... > search space = 74612.446501 > MatrixReadTxT: could not scan value [2][1] > > ERROR: loading C AAA.mtx > olof@olof-Latitude-E5430-non-vPro:/media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec$ > > > /Erik > > > On Thu, Nov 5, 2015 at 11:45 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > The contents of the AAA.mtx matrix are > > {1 1 1 1 -1 -1 -1 -1}/4 0 > > It has to be a simple matrix with simple numbers, no characters, > no math symbols. It will not do the math for you. > > > > On 11/05/2015 05:12 PM, Erik Lindberg wrote: > > Dear Doug, > attached is the folder I tried to run with the matrix. I also > put the .fsgd and the mtx file in the folder as well. > > most grateful for advice on this > > thanks! > > best Erik Lindberg > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > >

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interaction in glm
by Erik Lindberg 05 Nov '15

05 Nov '15

Dear Freesurfer experts, I know this has been an ongoing topic in the mailing list – however I would like to raise the issue one more time. In the choice between doss and dods – I usually check if there is a significant interaction and if so my choice is dods. As I understand it you do not recommend to use doss if an interaction is present. Is the reason for this that I would “over-correct” for the variable in one group while “under-correcting” for the same variable in the other group? It is some time tempting to present result both from a dods and a doss – to tell where the interaction is present, and where difference are present while controlling for the variable But if I understand Doug´s previous comments on this – this would not be a correct approach? Thanks Erik

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Re: [Freesurfer] the matrix
by Douglas N Greve 05 Nov '15

05 Nov '15

The contents of the AAA.mtx matrix are {1 1 1 1 -1 -1 -1 -1}/4 0 It has to be a simple matrix with simple numbers, no characters, no math symbols. It will not do the math for you. On 11/05/2015 05:12 PM, Erik Lindberg wrote: > Dear Doug, > attached is the folder I tried to run with the matrix. I also put the > .fsgd and the mtx file in the folder as well. > > most grateful for advice on this > > thanks! > > best Erik Lindberg -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer November 2015